• Kamieniarz-Gdula, K., Gdula, M.R., Panser, K., Nojima, T., Monks, J., Wisniewski, J.R., Riepsaame, J., Brockdorff, N., Pauli, A., Proudfoot, N.J. (2019). Selective roles of vertebrate PCF11 in premature and full-length transcript termination. Molecular Cell Apr 4;74(1):158-172.e9. doi:10.1016/j.molcel.2019.01.027


  • Herberg, S., Gert, K. R., Schleiffer, A., Pauli, A. (2018). The Ly6/uPAR protein Bouncer is necessary and sufficient for species-specific fertilization. Science 361(6406), 1029–1033. doi:10.1126/science.aat7113


  • Rogers, KW., Lord, ND., Gagnon, JA., Pauli, A., Zimmerman, S., Aksel, DC., Reyon, D., Tsai, SQ., Joung, JK., Schier, AF. (2017). Nodal patterning without Lefty inhibitory feedback is functional but fragile. eLife 6, e28785. doi:10.7554/eLife.28785

  • Freyer, L., Hsu, CW, Nowotschin, S., Pauli, A., Ishida, J., Kuba, K., Fukamizu, A., Schier, AF., Hoodless, PA., Dickinson, ME., Hadjantonakis, AK. (2017). Loss of Apela Peptide in Mice Causes Low Penetrance Embryonic Lethality and Defects in Early Mesodermal Derivatives. Cell Reports 20, 2116–2130. doi:10.1016/j.celrep.2017.08.014

  • Norris, ML., Pauli, A., Gagnon, JA., Lord, ND., Rogers, KW., Mosimann, C., Zon, LI., Schier, AF. (2017). Toddler signaling regulates mesodermal cell migration downstream of Nodal signaling. eLife 6, e22626. doi:10.7554/eLife.22626



  • Pauli, A., Valen, E., Schier, AF. (2015). Identifying (non-)coding RNAs and small peptides: challenges and opportunities. Bioessays 37(1):103-12. doi:10.1002/bies.201400103

  • Pauli, A., Montague, TG., Lennox, KA., Behlke, MA., Schier, AF. (2015). Antisense Oligonucleotide-Mediated Transcript Knockdown in Zebrafish. PLoS One 10(10):e0139504. doi:10.1371/journal.pone.0139504 | Pubmed:26436892


  • Pauli, A., Norris, ML., Valen, E., Chew, GL., Gagnon, JA., Zimmerman, S., Mitchell, A., Ma, J., Dubrulle, J., Reyon, D., Tsai, SQ., Joung, JK., Saghatelian, A., Schier, AF. (2014). Toddler: an embryonic signal that promotes cell movement via Apelin receptors. Science 343(6172):1248636. doi:10.1126/science.1248636 | Pubmed:24407481

  • Rabani, M., Raychowdhury, R., Jovanovic, M., Rooney, M., Stumpo, DJ., Pauli, A., Hacohen, N., Schier, AF., Blackshear, PJ., Friedman, N., Amit, I., Regev, A. (2014). High-resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies. Cell 159(7):1698-710. doi:10.1016/j.cell.2014.11.015 | Pubmed:25497548

  • Zhang, Y., Vastenhouw, NL., Feng, J., Fu, K., Wang, C., Ge, Y., Pauli, A., van Hummelen, P., Schier, AF., Liu, XS. (2014). Canonical nucleosome organization at promoters forms during genome activation. Genome Res 24(2):260-6. doi:10.1101/gr.157750.113 | Pubmed:24285721

  • Gagnon, JA., Valen, E., Thyme, SB., Huang, P., Akhmetova, L., Ahkmetova, L., Pauli, A., Montague, TG., Zimmerman, S., Richter, C., Schier, AF. (2014). Efficient mutagenesis by Cas9 protein-mediated oligonucleotide insertion and large-scale assessment of single-guide RNAs. PLoS One 9(5):e98186. doi:10.1371/journal.pone.0098186 | Pubmed:24873830


  • Chew, GL., Pauli, A., Rinn, JL., Regev, A., Schier, AF., Valen, E. (2013). Ribosome profiling reveals resemblance between long non-coding RNAs and 5’ leaders of coding RNAs. Development 140(13):2828-34. doi:10.1242/dev.098343 | Pubmed:23698349


  • Pauli, A., Valen, E., Lin, MF., Garber, M., Vastenhouw, NL., Levin, JZ., Fan, L., Sandelin, A., Rinn, JL., Regev, A., Schier, AF. (2012). Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. Genome Res 22(3):577-91. doi:10.1101/gr.133009.111 | Pubmed:22110045


  • Pauli, A., Rinn, JL., Schier, AF. (2011). Non-coding RNAs as regulators of embryogenesis. Nat Rev Genet 12(2):136-49. doi:10.1038/nrg2904 | Pubmed:21245830

  • Strübbe, G., Popp, C., Schmidt, A., Pauli, A., Ringrose, L., Beisel, C., Paro, R. (2011). Polycomb purification by in vivo biotinylation tagging reveals cohesin and Trithorax group proteins as interaction partners. Proc Natl Acad Sci U S A 108(14):5572-7. doi:10.1073/pnas.1007916108 | Pubmed:21415365


  • Pauli, A., van Bemmel, JG., Oliveira, RA., Itoh, T., Shirahige, K., van Steensel, B., Nasmyth, K. (2010). A direct role for cohesin in gene regulation and ecdysone response in Drosophila salivary glands. Curr Biol 20(20):1787-98. doi:10.1016/j.cub.2010.09.006 | Pubmed:20933422

  • Oliveira, RA., Hamilton, RS., Pauli, A., Davis, I., Nasmyth, K. (2010). Cohesin cleavage and Cdk inhibition trigger formation of daughter nuclei. Nat Cell Biol 12(2):185-92. doi:10.1038/ncb2018 | Pubmed:20081838


  • Pauli, A., Althoff, F., Oliveira, RA., Heidmann, S., Schuldiner, O., Lehner, CF., Dickson, BJ., Nasmyth, K. (2008). Cell-type-specific TEV protease cleavage reveals cohesin functions in Drosophila neurons. Dev Cell 14(2):239-51. doi:10.1016/j.devcel.2007.12.009 | Pubmed:18267092


  • Panse, VG., Kressler, D., Pauli, A., Petfalski, E., Gnädig, M., Tollervey, D., Hurt, E. (2006). Formation and nuclear export of preribosomes are functionally linked to the small-ubiquitin-related modifier pathway. Traffic 7(10):1311-21. doi:10.1111/j.1600-0854.2006.00471.x | Pubmed:16978391